Hi all.
I have population genetic diversity data (mtDNA) and am trying to use the software PERMUT (http://www.pierroton.inra.fr/genetics/labo/Software/Permut) as described theoretically by Pons and Petit (1996).
While the input data works fine and the output reveals the pretended values of hs, ht, Gst, Vs, Vt and Nst, they are given only for the whole dataset and not for each population.
Does this means there should be an input file for each population, having to input the data previously trimmed for variable sites, haplotypes and populations to have the values calculated? Or is there another way?
Thanks in advance
Ref:
Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics, 144, 1237–1245.
Since your study is on population genetics. There are lot of software's which does the analysis. For example ARELIQUIN, GENPOP, POPGENE, PAUP, GenAlex, STRUCTURE (All freely downloaded except PAUP). To make input files for these softwares, download CONVERT (a software) which makes input files form excel file. These softwares will solve your most of population genetics problems
Hi dear Artur
Powermarker is a good, perfect and easy, you can ddownload free.
Since your study is on population genetics. There are lot of software's which does the analysis. For example ARELIQUIN, GENPOP, POPGENE, PAUP, GenAlex, STRUCTURE (All freely downloaded except PAUP). To make input files for these softwares, download CONVERT (a software) which makes input files form excel file. These softwares will solve your most of population genetics problems
Hi Eduardo,
My understanding is that it is a single file that requires multiple populations in the columns where you are defining haplotype frequencies for each haplotype (above the block before where you define the variable sites in these haplotypes). The program (as far as I can tell) is calculating the values (GST, NST etc) over all the populations in your dataset (similar to an overall AMOVA FST). It wouldn't make sense to submit just a single population, because the program needs multiple populations to compare genetic differentiation (GST) to phylogeographic structure (NST). So, long story short, for each way you want to carve up your dataset, or 'zoom' in to look at specific subsets of the data, I believe you will have to create a separate input file e.g. I work on the sperm whale (globally distributed and found in each ocean): I carried out PERMUT at the oceanic level, then at a finer scale within oceans. I haven't found an easy way to create the files, but having a 'master file' which lists the haplotype codes next to the frequencies and to the haplotype definitions (and deleting these haplotype codes before running the file in PERMUT) can help with updating the numbers as you change your population definitions in the dataset.
Hope this helps!
Alana
PERMUTE is used to know the phylogeographic structure among different populations. You can use ARLIQUIN for both the regular markers and SSR.
Hi Eduardo,
I recently used Permut to test for phylogeographic signal in some populations of forest trees. As suggested by Alana, it would make no sense to compute a Gst and a Nst statistics if you have only one population, so you might have well made your input file. Moreover these statistics will not been given for each population, what you can compute at the population level is an allele diversity, an expected heterozigosity (even with haploid data... sic) or haplotype frequencies. There is another software that compute statistics useful for phylogeography, SPAGEDI, which is rather complete and offer more possibilities than permut to compute population-level statistics.
Good luck!
Hello!
I hope Eduardo solved his problem, I hope someone can help me as well...
I am using PERMUT for the first time. When i try to import my input file I constantly get the the message: "File not open. Press OK to ignore and risk data corruption. Press Cancel to kill the program." Is there something wrong with my input file? However, the same message appears when i try to import the example file...
Has this happened to anyone else?
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